Unit 3, Part 4

Question 1

What is DNA profiling?

Answer 1

To identify an individual from a sample by looking at the unique patterns in the DNA

Also known as DNA fingerprinting.

Question 2

What is the goal of DNA sequencing?

Answer 2

To determine the sequence of nucleotides in a DNA sample

This involves determining the exact order of nucleotides in a DNA molecule.

Question 3

What are the two main types of DNA analysis methods mentioned?

Answer 3

• DNA profiling or fingerprinting
• DNA sequencing

Question 4

What is Sanger sequencing known for?

Answer 4

Very accurate for small DNA segments (~1,000 bp)

Sanger sequencing is the first-generation sequencing method.

Question 5

What is the main advantage of Next Generation Sequencing (NGS)?

Answer 5

To read the whole genome

NGS allows for massively parallel sequencing.

Question 6

What are the two types of mapping discussed?

Answer 6

• Linkage mapping
• Physical mapping

Question 7

What does linkage mapping measure?

Answer 7

Based on recombination frequency

Measured in map units (relative distance).

Question 8

What does physical mapping measure?

Answer 8

Based on sequencing

Measured in base pairs (bp = actual position on chromosome).

Question 9

What are the key components set up in Sanger sequencing?

Answer 9

• DNA template (multiple copies)
• A primer
• DNA polymerase
• Normal dNTPs (all 4 bases)
• Labeled ddNTPs (one base/tube)

Question 10

What does NGS technology use for sequencing?

Answer 10

Fluorescently labeled chain-terminating nucleotides

These are used to identify the base at the end of each fragment.

Question 11

What is the biggest drawback of 2nd generation sequencing?

Answer 11

Only small fragments (35-200 bp)

This limits the assembly of longer sequences.

Question 12

What is a major advantage of 3rd generation sequencing?

Answer 12

Longer fragments (over 10,000 bp)

This facilitates easier assembly of sequences.

Question 13

What is genome assembly?

Answer 13

The process of taking many short DNA sequences and putting them back together to create a representation of the original chromosomes.

Question 14

What is the difference between reference-based assembly and de novo assembly?

Answer 14

• Reference-based: Uses a previously assembled reference genome to align reads
• De novo: Assembles from scratch without prior information

Question 15

What does ‘consensus sequence’ refer to?

Answer 15

Sequence of bases representing the majority of reads at a certain loci.

Question 16

What is genome annotation?

Answer 16

The process of identifying and describing the structure and function of a genome’s components.

Question 17

What is metagenomics?

Answer 17

Genetic analysis of genomes contained within an environmental sample.

Question 18

Fill in the blank: NGS allows sequencing of all the fragments at once, resulting in millions of _________.

Answer 18

reads

Question 19

What does 26X coverage mean?

Answer 19

Each base was sequenced, on average, 26 times.

Question 20

Is the reference sequence achieved at the end of genome assembly essentially a consensus sequence?

Answer 20

True

Question 21

What are some markers used in DNA profiling?

Answer 21

• Microsatellites
• SNPs

Question 22

What is the goal of structural genomic studies?

Answer 22

To focus on organization and sequence (order) of genes.

Question 23

What is the main focus of functional genomic studies?

Answer 23

Gene expression.

Question 24

What is a key challenge with assembling genomes?

Answer 24

Errors can occur during the sequencing or assembly process.